The 16S rRNA Illumina Miseq high-throughput sequencing technology was used to analyze the species composition of archaea in the Danjiangkou reservoir area and the downstream Hanjiang River. The structure of ammonia-oxidizing archaea (AOA) and methanogenic archaea that dominated the water and sediments in the upstream and downstream dam was analyzed. The results showed that the structure of the dominant species was affected by the samples difference, which could be explained by the aerobic preference of the ammonia-oxidizing archaea and the anaerobic properties of the methanogenic archaea. According to the network analysis, there was a significant correlation between the ammonia-oxidizing archaea and the methanogenic archaea in the upstream of the Danjiangkou reservoir. Because of the operation of the Danjiangkou reservoir, the abundance of ammoniaoxidizing archaea in the water and sediments of downstream of the dam was reduced, and the abundance of methanogenic archaea in the sediments was relatively high. The relation between them was not obvious.